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In the mirror universe, Starfleet Command was the organizational and command division of the Imperial Starfleet of the Terran Empire during the 22nd and 23rd centuries. (TOS episode: "Mirror, Mirror")
Like its primary universe counterpart, the Imperial Starfleet was controlled by a group of admirals, but was overseen by the Grand Admiral of the Imperial Starfleet. The commander in chief was in turn answerable to the Emperor of the Terran Empire. (TOS - Mirror Universe novel: The Sorrows of Empire)
In 2155, Commander Jonathan Archer claimed to have received a private communiqué from Starfleet Command when he took over the command of the ISS Enterprise (NX-01). He later blamed the rebellion on "criminals... sitting in their comfortable offices back at Starfleet Command." (ENT episode: "In a Mirror, Darkly")
In 2267, Captain James T. Kirk of the primary universe (impersonating his mirror universe counterpart) defied orders from Starfleet Command by delaying the destruction the Halkans. Starfleet Command then ordered Spock to wait one day to see if Kirk would follow his orders and then to kill him if he did not so, becoming the new captain of the ISS Enterprise (NCC-1701). (TOS episode: "Mirror, Mirror")